Q1. What have the authors contributed in "Flexible protein–protein docking" ?
In this paper, the authors proposed a method for the explicit inclusion of backbone flexibility in docking, which should allow larger conformational changes to be modeled.
Flexible protein-protein docking.
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TLDR
Although significant improvements have been achieved in the modeling of sidechains, methods for the explicit inclusion of backbone flexibility in docking are still being developed, and a few novel approaches have emerged involving collective degrees of motion, multicopy representations and multibody docking, which should allow larger conformational changes to be modeled.About:
This article is published in Current Opinion in Structural Biology.The article was published on 2006-04-01 and is currently open access. It has received 301 citations till now. The article focuses on the topics: Searching the conformational space for docking & Protein–ligand docking.read more
Citations
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The HADDOCK web server for data-driven biomolecular docking
TL;DR: The HADDOCK web server protocol is presented, facilitating the modeling of biomolecular complexes for a wide community, and has access to the resources of a dedicated cluster and of the e-NMR GRID infrastructure.
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X-ray solution scattering (SAXS) combined with crystallography and computation: defining accurate macromolecular structures, conformations and assemblies in solution.
TL;DR: In this article, a review of the use of small angle X-ray scattering (SAXS) for modeling macromolecular folding, unfolding, aggregation, extended conformations, flexibly linked domains, shape, conformation, and assembly state in solution, albeit at the lower resolution range of about 50 A to 10 A resolution, is presented.
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FireDock: a web server for fast interaction refinement in molecular docking
TL;DR: The FireDock web server, presented here, is the first web server for flexible refinement and scoring of protein–protein docking solutions and includes optimization of side-chain conformations and rigid-body orientation and allows a high-throughput refinement.
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HADDOCK versus HADDOCK: new features and performance of HADDOCK2.0 on the CAPRI targets.
Sjoerd J. de Vries,Aalt D. J. van Dijk,Mickaël Krzeminski,Marc van Dijk,Aurelien Thureau,Victor L. Hsu,Tsjerk A. Wassenaar,Alexandre M. J. J. Bonvin +7 more
TL;DR: HADDOCK2.0 as mentioned in this paper is the most recent version of HADDOCK, which incorporates considerable improvements and new features, such as random patch definition or center-of-mass restraints.
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Combining an Elastic Network With a Coarse-Grained Molecular Force Field: Structure, Dynamics, and Intermolecular Recognition
TL;DR: The results for this series of tests indicate that ELNEDIN models allow microsecond time-scale molecular dynamics simulations to be carried out readily, that large biological entities such as the viral capsid of the cowpea mosaic virus can be stably modeled as assemblies of independent ELNedIN models, and that ELnEDin models show significant promise for modeling protein-protein association processes.
References
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Essential dynamics of proteins
TL;DR: Analysis of extended molecular dynamics simulations of lysozyme in vacuo and in aqueous solution reveals that it is possible to separate the configurational space into two subspace: an “essential” subspace containing only a few degrees of freedom and the remaining space in which the motion has a narrow Gaussian distribution and which can be considered as “physically constrained.”
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HADDOCK: a protein-protein docking approach based on biochemical or biophysical information.
TL;DR: An approach called HADDOCK (High Ambiguity Driven protein-protein Docking) that makes use of biochemical and/or biophysical interaction data such as chemical shift perturbation data resulting from NMR titration experiments or mutagenesis data to drive the docking process.
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Large Amplitude Elastic Motions in Proteins from a Single-Parameter, Atomic Analysis.
TL;DR: It is shown that a single-parameter potential is sufficient to reproduce the slow dynamics of proteins obtained with vastly more complex empirical potentials, which inevitably leads to unstable modes which must be eliminated through elaborate methods, and which cast doubts on the validity of the analysis.
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Protein-protein docking with simultaneous optimization of rigid-body displacement and side-chain conformations.
Jeffrey J. Gray,Stewart E. Moughon,Chu Wang,Ora Schueler-Furman,Brian Kuhlman,Carol A. Rohl,David Baker +6 more
TL;DR: A new method to predict protein-protein complexes from the coordinates of the unbound monomer components using a low-resolution, rigid-body, Monte Carlo search followed by simultaneous optimization of backbone displacement and side-chain conformations using Monte Carlo minimization is presented.
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Protein flexibility predictions using graph theory
TL;DR: This novel computational procedure is approximately a million times faster than molecular dynamics simulations and captures the essential conformational flexibility of the protein main and side‐chains from analysis of a single, static three‐dimensional structure.